The ultimate goal of proteomics is determination of the functions of genes from analysis of the proteome and its response to perturbations. Inferences about gene and pathway function can be obtained using a broad range of proteomics technologies, from classical protein expression profiling to yeast two-hybrid methodologies and high-throughput analysis of protein complexes. One of the most useful conceptual approaches in proteomics is to elucidate pathways and identify control points in those pathways. This can be achieved by combining data from current and emerging proteomics technologies to establish functional linkages between proteins, for example, by determining direct interactions, genetic interactions, and coordinate expression profiles. This proposal describes technologies that allow improvements in proteome mapping, methods to query changes in signal transduction, identification of protein interactions, and improved algorithms and computational tools for analyzing proteomics data. Altogether, they represent an integrated approach to identifying and building maps of cell pathways. Specific new technology areas addressed include: phosphoproteomics, high-throughput isolation of protein complexes, high-throughput yeast two-hybrid technologies, virtual 2D gels, protein microarrays, and collision-induced-dissociation of proteins. Mechanisms are proposed to provide dissemination of results, provide training opportunities, and ensure that technology development is responsive to the needs of investigators. One of the strengths of this proposal is its potential to leverage the substantial investment in proteomics infrastructure made by the State of Michigan and to extend the benefits of this investment to investigators outside Michigan.